Novel Alphacoronaviruses and Paramyxoviruses Cocirculate with Type 1 and Severe Acute Respiratory System (SARS)-Related Betacoronaviruses in Synanthropic Bats of Luxembourg

Abstract

Several infectious disease outbreaks with high mortality in humans have been attributed to viruses that are thought to have evolved from bat viruses. In this study from Luxembourg, the genetic diversity and epidemiology of paramyxoviruses and coronaviruses shed by the bat species <i>Rhinolophus ferrumequinum</i> and <i>Myotis emarginatus</i> were evaluated. Feces collection (<i>n</i> = 624) was performed longitudinally in a mixed-species colony in 2015 and 2016. In addition, feces (<i>n</i> = 254) were collected cross-sectionally from six <i>Myotis emarginatus</i> colonies in 2016. By use of degenerate primers in a nested format, overall prevalences of 1.1% (10/878) and 4.9% (43/878) were determined for paramyxoviruses and coronaviruses. Sequences of the partial RNA-dependent RNA polymerase and spike glycoprotein genes of coronaviruses, as well as sequences of the partial L gene of paramyxoviruses, were obtained. Novel paramyxovirus and <i>Alphacoronavirus</i> strains were identified in different <i>Myotis emarginatus</i> colonies, and severe acute respiratory syndrome (SARS)-related <i>Betacoronavirus</i> strains were shed by <i>Rhinolophus ferrumequinum</i> Logistic regression revealed that the level of <i>Alphacoronavirus</i> shedding was highest in July (odds ratio, 2.8; <i>P</i> < 0.01), probably due to periparturient stress. Phylogenetic analyses point to close virus-host coevolution, and the high genetic similarity of the study strains suggests that the <i>Myotis emarginatus</i> colonies in Luxembourg are socially connected. Most interestingly, we show that bats also host <i>Betacoronavirus</i><i>1</i> strains. The high similarity of the spike gene sequences of these viruses with mammalian <i>Betacoronavirus 1</i> strains may be of concern. Both the SARS-related and <i>Betacoronavirus 1</i> strains detected in bats in Luxembourg may cross the species barrier after a host adaptation process.<b>IMPORTANCE</b> Bats are a natural reservoir of a number of zoonotic pathogens. Several severe outbreaks in humans (e.g., a Nipah virus outbreak in Malaysia in 1998, and the almost global spread of severe acute respiratory syndrome in 2003) have been caused by bat-borne viruses that were transmitted to humans mostly after virus adaptation (e.g., in intermediate animal hosts). Despite the indigenousness of bat species that host viruses with suspected zoonotic potential and despite the zoonotic transmission of European bat 1 lyssavirus in Luxembourg, knowledge about the diversity and epidemiology of bat viruses remains limited in this country. Moreover, in contrast to other European countries, bat viruses are currently not included in the national surveillance activities of this land-locked country. We suggest that this gap in disease surveillance should be addressed, since we show here that synanthropic bats host viruses that may be able to cross the species barrier.